Advanced NFL Stats has an unique approach to stats.
It adds the element of probability.

For example WPA/Game is the Win Probability Added Value of a player (in this case, the QB). It gives you how much quality you get from your QB that helps you win the game.

When you look at this number (since a QB might be injured and didn't play the whole season), it shows that Schaub have had more better games than Flacco since 07, even though Flacco did have a couple of years where he was ahead of Schaub in this measure.

However, keep in mind that WPA is somewhat dependent on the defense and ST play.

There's another measure called EPA/P (Expected Point Added per Play).
It tries to depict how each QB's individual play helps add points to his team.
By this measure, Schaub has been consistently much better than Flacco.

These don't tell you how good the protections are or how much the receivers help or hurt the QBs.

No matter what, it gives you a broad view of the abilities of these guys if you add a whole career together.